SMTL ID : 9cu2.1

Azotobacter vinelandii filamentous 2:2:1 MoFeP:FeP:FeSII-Complex (C2 symmetry)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-4-1-1-mer

Ligands

4 x HCA: 3-HYDROXY-3-CARBOXY-ADIPIC ACID(Non-covalent)

HCA.1: 9 residues within 4Å: Chain A: A.65, G.95, R.96, Q.191, G.424, I.425, H.442 Chain B: R.105 Ligands: ICS.2 11 PLIP interactions: 8 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.191, A:I.425, A:H.442 Water bridges: A:K.426, A:K.426, A:K.426, B:Y.98, B:R.105, B:R.105 Salt bridges: A:K.426, A:H.442 HCA.6: 10 residues within 4Å: Chain C: A.65, V.70, G.95, R.96, Q.191, G.424, I.425, K.426, H.442 Ligands: ICS.7 8 PLIP interactions: 1 interactions with chain D, 7 interactions with chain C Water bridges: D:R.105, C:K.426, C:K.426, C:E.440 Hydrogen bonds: C:Q.191, C:I.425 Salt bridges: C:K.426, C:H.442 HCA.15: 9 residues within 4Å: Chain H: A.65, G.95, R.96, Q.191, G.424, I.425, K.426, H.442 Ligands: ICS.16 10 PLIP interactions: 2 interactions with chain I, 8 interactions with chain H Water bridges: I:Y.98, I:R.105, H:E.380, H:K.426 Hydrophobic interactions: H:H.442 Hydrogen bonds: H:Q.191, H:I.425, H:H.442 Salt bridges: H:K.426, H:H.442 HCA.19: 9 residues within 4Å: Chain J: A.65, R.96, Q.191, E.380, G.424, I.425, K.426, H.442 Ligands: ICS.20 9 PLIP interactions: 9 interactions with chain J Hydrogen bonds: J:Q.191, J:I.425, J:K.426, J:H.442 Water bridges: J:K.426, J:K.426 Salt bridges: J:K.426, J:H.442, J:H.442

4 x ICS: iron-sulfur-molybdenum cluster with interstitial carbon(Non-covalent)

ICS.2: 13 residues within 4Å: Chain A: V.70, R.96, H.195, Y.229, I.231, C.275, S.278, I.355, G.357, R.359, F.381, H.442 Ligands: HCA.1 2 PLIP interactions: 2 interactions with chain A, Salt bridges: A:E.380 Metal complexes: A:C.275 ICS.7: 15 residues within 4Å: Chain C: V.70, R.96, H.195, Y.229, I.231, C.275, S.278, I.355, G.356, G.357, L.358, R.359, F.381, H.442 Ligands: HCA.6 2 PLIP interactions: 2 interactions with chain C, Salt bridges: C:E.380 Metal complexes: C:C.275 ICS.16: 15 residues within 4Å: Chain H: V.70, R.96, H.195, Y.229, I.231, C.275, S.278, I.355, G.356, G.357, L.358, R.359, F.381, H.442 Ligands: HCA.15 2 PLIP interactions: 2 interactions with chain H, Salt bridges: H:E.380 Metal complexes: H:C.275 ICS.20: 13 residues within 4Å: Chain J: V.70, R.96, H.195, Y.229, I.231, C.275, S.278, G.356, L.358, R.359, F.381, H.442 Ligands: HCA.19 2 PLIP interactions: 2 interactions with chain J, Salt bridges: J:E.380 Metal complexes: J:C.275

4 x FE: FE (III) ION(Non-covalent)

FE.3: 4 residues within 4Å: Chain B: D.353, D.357 Chain D: R.108, E.109 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B Metal complexes: D:R.108, D:E.109, B:D.353, B:D.357 FE.5: 5 residues within 4Å: Chain A: K.433 Chain B: R.108, E.109 Chain D: D.353, D.357 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D Metal complexes: B:R.108, B:E.109, D:D.353, D:D.357 FE.18: 4 residues within 4Å: Chain I: D.353, D.357 Chain K: R.108, E.109 4 PLIP interactions: 2 interactions with chain K, 2 interactions with chain I Metal complexes: K:R.108, K:E.109, I:D.353, I:D.357 FE.21: 4 residues within 4Å: Chain I: R.108, E.109 Chain K: D.353, D.357 4 PLIP interactions: 2 interactions with chain I, 2 interactions with chain K Metal complexes: I:R.108, I:E.109, K:D.353, K:D.357

4 x CLF: FE(8)-S(7) CLUSTER(Non-covalent)

CLF.4: 19 residues within 4Å: Chain A: C.62, Y.64, P.85, G.87, C.88, Y.91, E.153, C.154, G.185 Chain B: C.70, P.72, S.92, G.94, C.95, Y.98, F.99, T.152, C.153, S.188 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain B, Salt bridges: A:E.153 Metal complexes: A:C.62, A:C.88, A:C.88, A:C.154, B:C.70, B:C.95, B:C.95, B:C.153, B:S.188 CLF.8: 16 residues within 4Å: Chain C: C.62, Y.64, P.85, G.87, C.88, Y.91, C.154, G.185 Chain D: C.70, P.72, S.92, G.94, C.95, Y.98, C.153, S.188 9 PLIP interactions: 4 interactions with chain C, 5 interactions with chain D, Salt bridges: C:E.153 Metal complexes: C:C.62, C:C.88, C:C.154, D:C.70, D:C.95, D:C.95, D:C.153, D:S.188 CLF.17: 19 residues within 4Å: Chain H: C.62, Y.64, P.85, G.87, C.88, Y.91, E.153, C.154, G.185 Chain I: C.70, P.72, S.92, G.94, C.95, Y.98, F.99, T.152, C.153, S.188 10 PLIP interactions: 5 interactions with chain H, 5 interactions with chain I, Salt bridges: H:E.153 Metal complexes: H:C.62, H:C.88, H:C.88, H:C.154, I:C.70, I:C.95, I:C.95, I:C.153, I:S.188 CLF.22: 18 residues within 4Å: Chain J: C.62, Y.64, P.85, G.87, C.88, Y.91, C.154, G.185 Chain K: C.70, P.72, S.92, G.94, C.95, Y.98, F.99, T.152, C.153, S.188 9 PLIP interactions: 4 interactions with chain K, 5 interactions with chain J, Metal complexes: K:C.70, K:C.95, K:C.153, K:S.188, J:C.62, J:C.88, J:C.88, J:C.154 Salt bridges: J:E.153

4 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.9: 15 residues within 4Å: Chain E: G.12, G.13, I.14, G.15, K.16, S.17, T.18, N.186, P.213, R.214, D.215, V.218, Q.219, Y.241 Ligands: MG.10 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:G.13, E:I.14, E:G.15, E:K.16, E:S.17, E:S.17, E:T.18, E:N.186, E:R.214, E:D.215, E:Q.237 Salt bridges: E:K.16 ADP.12: 16 residues within 4Å: Chain F: G.12, G.13, I.14, G.15, K.16, S.17, T.18, V.212, R.214, D.215, V.218, Q.219, E.222, Q.237, Y.241 Ligands: MG.13 15 PLIP interactions: 15 interactions with chain F Hydrogen bonds: F:G.13, F:I.14, F:G.15, F:K.16, F:S.17, F:T.18, F:T.18, F:D.215, F:Q.219, F:E.222, F:Q.237, F:Y.241 Water bridges: F:K.42, F:R.214 Salt bridges: F:K.16 ADP.23: 19 residues within 4Å: Chain L: G.12, G.13, I.14, G.15, K.16, S.17, T.18, K.42, D.44, V.212, P.213, R.214, D.215, V.218, Q.219, E.222, Q.237, Y.241 Ligands: MG.24 16 PLIP interactions: 16 interactions with chain L Hydrogen bonds: L:G.13, L:I.14, L:G.15, L:K.16, L:S.17, L:T.18, L:D.215, L:D.215, L:Q.219, L:E.222, L:Q.237 Water bridges: L:T.18, L:T.18 Salt bridges: L:K.16, L:K.42, L:K.42 ADP.26: 17 residues within 4Å: Chain L: M.157 Chain M: G.12, G.13, I.14, G.15, K.16, S.17, T.18, N.186, V.212, R.214, D.215, V.218, E.222, Q.237, Y.241 Ligands: MG.27 15 PLIP interactions: 15 interactions with chain M Hydrogen bonds: M:G.13, M:I.14, M:G.15, M:K.16, M:S.17, M:T.18, M:T.18, M:N.186, M:D.215, M:E.222, M:Q.237, M:Y.241 Water bridges: M:K.42, M:R.214 Salt bridges: M:K.16

4 x MG: MAGNESIUM ION(Non-covalent)

MG.10: 3 residues within 4Å: Chain E: S.17, K.42 Ligands: ADP.9 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:S.17 MG.13: 4 residues within 4Å: Chain F: S.17, D.40, D.44 Ligands: ADP.12 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:S.17 MG.24: 4 residues within 4Å: Chain L: S.17, K.42, D.44 Ligands: ADP.23 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:S.17, L:D.44 MG.27: 4 residues within 4Å: Chain M: S.17, D.40, D.44 Ligands: ADP.26 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:S.17

2 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.11: 12 residues within 4Å: Chain E: C.98, A.99, G.100, C.133, G.134, F.136 Chain F: C.98, C.133, G.134, F.136 Chain G: P.119, A.122 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain F, Metal complexes: E:C.98, E:C.133, F:C.98, F:C.133 SF4.25: 13 residues within 4Å: Chain L: C.98, A.99, C.133, G.134, F.136 Chain M: G.97, C.98, A.99, C.133, G.134, F.136 Chain N: P.119, A.122 4 PLIP interactions: 2 interactions with chain L, 2 interactions with chain M, Metal complexes: L:C.98, L:C.133, M:C.98, M:C.133

2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.14: 9 residues within 4Å: Chain G: F.40, E.41, C.42, G.45, N.46, C.47, G.48, C.50, C.102 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.42, G:C.47, G:C.50, G:C.102 FES.28: 9 residues within 4Å: Chain N: F.40, E.41, C.42, G.45, C.47, S.49, C.50, C.102, Q.103 4 PLIP interactions: 4 interactions with chain N, Metal complexes: N:C.42, N:C.47, N:C.50, N:C.102

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Narehood, S.M. et al., Structural basis for the conformational protection of nitrogenase from O 2 . Nature (2025)

Release Date

2025-01-15

Peptides

Nitrogenase molybdenum-iron protein alpha chain: ACHJ
Nitrogenase molybdenum-iron protein beta chain: BDIK
Nitrogenase iron protein 1: EFLM
Protein FeSII: G
Protein FeSII: N

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

H
H

J
J

B
B

D
D

I
I

K
K

E
E

F
F

L
L

M
M

G
G

N
N

Nitrogenase molybdenum-iron protein alpha chain

Nitrogenase molybdenum-iron protein beta chain

Nitrogenase iron protein 1

Protein FeSII

Protein FeSII

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